long-read-sequencing

There are 1 repository under long-read-sequencing topic.

google / deepconsensus
DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
bioinformatics transformers deep-learning long-read-sequencing
Language:Python 216
nf-core / mag
Assembly and binning of metagenomes
workflow nextflow metagenomics assembly binning annotation nf-core pipeline bioinformatics nanopore nanopore-sequencing metagenomes long-read-sequencing
Language:Nextflow 183
nf-core / viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
viral metagenomics amplicon assembly variant-calling illumina pipeline workflow nextflow nf-core covid-19 covid19 virus sars-cov-2 nanopore ont artic long-read-sequencing oxford-nanopore
Language:Nextflow 110
ksahlin / ultra
Long-read splice alignment with high accuracy
bioinformatics long-read-sequencing alignment strobemers
Language:Python 59
HKU-BAL / ClairS
ClairS - a deep-learning method for long-read somatic small variant calling
deep-learning long-reads nanopore ont somatic-mutations somatic-variants bioinformatics genomics haplotypes phasing snvs indels illumina long-read-sequencing short-reads pacbio
Language:Python 56
katerinakazantseva / strainy
Graph-based assembly phasing
assembly hifi long-read-sequencing long-reads metagenomic-analysis metagenomics nanopore sequencing
Language:Python 42
HudsonAlpha / fmlrc2
rust genomics long-read-sequencing error-correction bwt
Language:Rust 41
BeatsonLab-MicrobialGenomics / micropipe
A pipeline for high-quality bacterial genome construction using ONT sequencing
genome-assembly long-read-sequencing nanopore-analysis-pipeline bioinformatics-pipeline microbial-genomics oxford-nanopore
Language:HTML 38
sheynkman-lab / Long-Read-Proteogenomics
A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.
pipeline proteomics long-read-sequencing isoforms nextflow
Language:Python 37
noush-joglekar / scisorseqr
scisorseqr is an R-package for processing of single-cell long read data and analyzing differential isoform expression across any two conditions
differential-analysis long-read-sequencing single-cell-rna-seq splicing-quantification
Language:R 34
gaolabtools / scNanoGPS
Single cell Nanopore sequencing data for Genotype and Phenotype
cell-barcode demultiplexing gene-expression isoforms long-read-sequencing nanopore-analysis-pipeline rna-seq-pipeline single-cell single-nucleotide-variation umi-curation
Language:Python 33
Serka-M / mmlong2
Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
bioinformatics metagenomics metagenome-assembled-genomes nanopore pacbio long-read-sequencing microbial-genomics microbiome
Language:Python 33
HKU-BAL / ClairS-TO
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
bioinformatics deep-learning genomics illumina long-read-sequencing long-reads nanopore ont pacbio snvs somatic-mutations somatic-variants tumor-only tumors variant-calling variants
Language:Python 32
bcgsc / goldrush
Linear-time de novo Long Read Assembler
bioinformatics bioinformatics-tool genome-assembly long-read-sequencing
Language:C++ 30
nanome
LabShengLi / nanome
NANOME pipeline (Nanopore long-read sequencing data consensus DNA methylation detection)
dna-methylation long-read-sequencing nanopore-sequencing methylation-calling bioinformatics pipeline
Language:Python 29
monarch-initiative / SvAnna
Efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing
genomics long-read-sequencing prioritization bioinformatics rare-disease
Language:Java 29
Nazeeefa / awesome-sequencing-tech-papers
A collection of publications on comparison of high-throughput sequencing technologies.
nanopore pacbio illumina genomics sequencing bioinformatics sequence-alignment genome-sequencing dna-sequencing awesome-list human-genomes hifi long-read-sequencing illumina-sequencing
26
seryrzu / centroFlye
An algorithm for centromere assembly using long error-prone reads
genome-assembly genomics long-reads long-read-sequencing centromere
Language:Python 26
tseemann / berokka
🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
circular-genome bioinformatics genomics genome-assembly long-read-sequencing
Language:Perl 25
tobiasrausch / lorax
A long-read analysis toolbox for cancer and population genomics
long-reads long-read-sequencing cancer-genomics genomics bioinformatics telomere amplicon
Language:C++ 19
JensUweUlrich / Taxor
Fast and space-efficient taxonomic classification of long reads
kmer long-read long-read-sequencing metagenomics syncmer taxonomic-classification taxonomic-profiling bioinf em-algorithm pseudo-alignment xor-filter interleaved-xor-filter bioinformatics microbiome refseq taxonomy
Language:C++ 16
edgecase
LankyCyril / edgecase
A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.
telomeres haplotypes repeats genomics bioinformatics bioinformatics-pipeline genomics-visualization long-reads long-read-sequencing
Language:Python 14
josiegleeson / BamSlam
Summarise and plot data from long-read ONT (direct RNA/cDNA) BAM files
bioinformatics direct-rna-sequencing long-read-sequencing
Language:R 11
CoSA
Magdoll / CoSA
Coronavirus (SARS-Cov-2) sequencing analysis
sars-cov-2 pacbio long-reads long-read-sequencing covid19
Language:Python 10
comprna / reorientexpress
Transcriptome long-read orientation with Deep Learning
long-read-sequencing nanopore-sequencing deep-learning convolutional-neural-networks multilayer-perceptron-network machine-learning
Language:Python 9
HKU-BAL / Clair3-RNA
Clair3-RNA - a long-read small variant caller for RNA sequencing data
deep-learning long-read-sequencing nanopore ont pacbio-iso-seq rna rna-editing rna-seq rna-seq-pipeline variant-calling
Language:Python 8
kaist-ina / RUN-DVC
Generalizing deep learning-based variant callers via domain adaptation and semi-supervised learning
deep-learning domain-adaptation generalization long-read-sequencing ngs semi-supervised-learning variant-calling bioinformatics dna-sequencing transfer-learning genomics
Language:Python 8
dyxstat / MetaCC
MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data
hi-c metagenomics long-read-sequencing
Language:C 7
yanhui09 / laca
A reproducible and scalable workflow for Long Amplicon Consensus Analysis (LACA)
denoise nanopore amplicon long-read-sequencing
Language:Python 7
DrQuestion / monica
MinION Open-source Nucleotide Identifier for Continuous Analysis - Software for MinION sequencing quantitative metagenomic analysis in real time
long-read-sequencing metagenomics minion-sequencer pathology pathobiomics
Language:Python 5
nf-core / scnanoseq
Single-cell/nuclei pipeline for data derived from Oxford Nanopore
10xgenomics long-read-sequencing nanopore nextflow nf-core scrna-seq single-cell
Language:Nextflow 5
akikuno / DAJIN2
🔬 Genotyping tool for genome-edited samples, utilizing nanopore sequencer target sequencing
bioinformatics crispr-target genomics long-read-sequencing python3 nanopore
Language:Python 4
quadram-institute-bioscience / galaxy-tools
A collection of bioinformatics tools for use with galaxy written at Quadram Institute
galaxy bioinformatics mlst long-read-sequencing nanopore pacbio amr biotradis plasmid
Language:HTML 4
Serka-M / mmlong2-lite
Lightweight bioinformatics pipeline for microbial genome recovery
bioinformatics long-read-sequencing metagenome-assembled-genomes metagenomics microbial-genomics microbiome nanopore pacbio singularity-container snakemake-workflow
Language:Python 4
seryrzu / centroFlye_paper_scripts
Scripts for the Nature Biotechnology paper, 2020: Automated assembly of centromeres from ultra-long error-prone reads
genome-assembly genomics long-reads long-read-sequencing centromere
Language:Jupyter Notebook 4
baigal628 / NEMO
a deep neural network model for mapping modifications in nanopore Long-read sequencing data
epig long-read-sequencing nanopore-sequencing
Language:Python 3